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secondMigration.R
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secondMigration.R
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#leave some breadcrumbs...
#mayo rnaseq
source('RFunctions/populateNewDirectory2.R')
source('RFunctions/makeNewFolder.R')
source('RFunctions/makeLink.R')
source('RFunctions/crawlSynapseObject.R')
source('RFunctions/makeHeadFolder.R')
source('RFunctions/adjacentEdges.R')
##RNASEQ Mayo
synObj <- crawlSynapseObject('syn3163039')
synObj <- makeHeadFolder(synObj,'syn3163039')
synLinks <- populateNewDirectory2('syn2924460',synObj,topId='syn2924460')
##RNASEQ UFL App
synObj <- crawlSynapseObject('syn3435792')
synObj <- makeHeadFolder(synObj,'syn3435792')
synLinks <- populateNewDirectory2('syn2924458',synObj,topId='syn2924458')
##Emory
synObj <- crawlSynapseObject('syn3606086')
synObj <- makeHeadFolder(synObj,'syn3606086')
synLinks <- populateNewDirectory2('syn2920322',synObj,topId='syn2920322')
##Myers Data
synObj <- crawlSynapseObject('syn3800853')
synObj <- makeHeadFolder(synObj,'syn3800853')
synLinks <- populateNewDirectory2('syn2700793',synObj,topId='syn2700793')
##Broad MDMi data
synObj <- crawlSynapseObject('syn3607404')
synObj <- makeHeadFolder(synObj,'syn3607404')
mdmiF <- synGet('syn3607404',downloadFile=F)
anno <- synGetAnnotations(mdmiF)
mdmi <- synGet('syn3607432',downloadFile=F)
synSetAnnotations(mdmi)<- as.list(anno)
mdmi <- synStore(mdmi,forceVersion=F)
mdmi <- synGet('syn3607433',downloadFile=F)
synSetAnnotations(mdmi)<- as.list(anno)
mdmi <- synStore(mdmi,forceVersion=F)
synLinks <- populateNewDirectory2('syn2397884',synObj,topId='syn2397884')
##Broad iPSC data
synObj <- crawlSynapseObject('syn3607401')
synObj <- makeHeadFolder(synObj,'syn3607401')
mdmiF <- synGet('syn3607401',downloadFile=F)
anno <- synGetAnnotations(mdmiF)
mdmi <- synGet('syn3607402',downloadFile=F)
synSetAnnotations(mdmi)<- as.list(anno)
mdmi <- synStore(mdmi,forceVersion=F)
mdmi <- synGet('syn3607403',downloadFile=F)
synSetAnnotations(mdmi)<- as.list(anno)
mdmi <- synStore(mdmi,forceVersion=F)
synLinks <- populateNewDirectory2('syn2397884',synObj,topId='syn2397884')
##Broad miRNA data
mirnaf <- synGet('syn3387325',downloadFile=F)
anno <- synGetAnnotations(mirnaf)
mirna <- synGet('syn3387327',downloadFile=F)
synSetAnnotations(mirna) <- as.list(anno)
mirna <- synStore(mirna,forceVersion=F)
synObj <- crawlSynapseObject('syn3387325')
synObj <- makeHeadFolder(synObj,'syn3387325')
synLinks <- populateNewDirectory2('syn2700793',synObj,topId='syn2700793')
##HBTRC imputed genotype data
synObj <- crawlSynapseObject('syn3981980')
synObj <- makeHeadFolder(synObj,'syn3981980')
synLinks <- populateNewDirectory2('syn3104310',synObj,topId='syn3104310')
##move apoe genotypes
#move broad-rush covariates
synObj <- File('~/Desktop//AMP-AD_ROSMAP_Myers-RUSH-NIAGADS_Covariates.csv',parentId='syn3800853')
anno <- list(center='Myers-NIAGADS',
dataType='Covariates',
consortium='AMP-AD',
fileType='csv',
study='ROSMAP',
disease='Alzheimers Disease, Control',
organism='Homo Sapiens')
synSetAnnotations(synObj) <- anno
synObj <- synStore(synObj)
#move .bam files
synObj <- crawlSynapseObject('syn4055270')
synObj <- makeHeadFolder(synObj,'syn4055270')
synLinks <- populateNewDirectory2('syn3104300',synObj,topId='syn3104310')
##move ROSMAP rna-seq data
synObj <- crawlSynapseObject('syn3388564')
headFolder <- synGet('syn3388564',downloadFile = F)
anno <- synGetAnnotations(headFolder)
rnaExprSyn <- names(which(synObj$adj[1,]!=0)[1:6])
#add annotations to rnaseq files
lapply(rnaExprSyn,function(x,anno){ob<-synGet(x,downloadFile=F);synSetAnnotations(ob)<-as.list(anno);ob <- synStore(ob,forceVersion=F);},anno)
anno <- as.list(anno)
anno$dataSubType <- NULL
anno$dataType <- "metaData"
#add annotations to picard files
metricFile <- c(names(which(synObj$adj[10,]!=0)),'syn4299317')
lapply(metricFile,function(x,anno){ob<-synGet(x,downloadFile=F);synSetAnnotations(ob)<-as.list(anno);ob <- synStore(ob,forceVersion=F);},anno)
#
synObj <- makeHeadFolder(synObj,'syn3388564')
synLinks <- populateNewDirectory2('syn2700793',synObj,topId='syn2700793')